Harvard Medical School assistant professor Soumya Raychaudhuri runs a lab looking to cure tuberculosis and rheumatoid arthritis. On Saturday, his new research assistant was not allowed to board a plane to Boston because she is Iranian. (Kirk Carapezza/WGBH)

At the Massachusetts Institute of Technology, where over 40 percent of the faculty and graduate students are foreign-born, administrators and faculty gathered on Sunday to protest President Donald Trump’s executive order.

“I think everyone is very deeply concerned,” said Mohammad Alizadh, an associate professor in MIT’s Department of Electrical Engineering and Computer Science. “At the senior levels of the Institute and more within each department, I don’t think anyone’s taking this lightly.”

Colleges and universities across the country are scrambling to deal with Trump’s temporary travel ban on citizens of seven Muslim-majority countries linked to concerns about terrorism.

Hours before her flight to Boston on Saturday, Harvard Medical School student Samira Asgari says a U.S. border agent in Frankfurt, Germany blocked her from entering the country because she’s Iranian.

“When I told him that I have a valid visa, he told me that it’s the American government who provides the visas, and they can change their mind any minute they want,” Asgari, 30, said via Skype in Switzerland.

After earning her Ph.D. there at the École Polytechnique Fédérale de Lausanne, Asgari had been accepted as a post-doctorate at Harvard Medical School. It was her dream research position.

“I knew that I wanted to go to Boston after my Ph.D. for my training because it’s one of the greatest places for science in general but especially in my field, which is genomics,” Asgari said. “Boston really offers a unique opportunity for learning.”

Since Trump's executive order went into effect on Friday, concrete implications of the new travel restrictions remain unclear. Still, Harvard has quietly been advising international students here and abroad and urging them to “assess whether it is worth the risk to travel outside the country.”

In a letter sent to the campus community Sunday afternoon, Harvard President Drew Faust strongly rebuked Trump’s travel ban.

“Nearly half of the deans of Harvard’s schools are immigrants — from India, China, Northern Ireland, Jamaica, and Iran,” Faust wrote. “Benefiting from the talents and energy, the knowledge and ideas of people from nations around the globe is not just a vital interest of the University, it long has been, and it fully remains, a vital interest of our nation.”

Harvard isn’t alone. Northeastern, Tufts, Boston University and the University of Massachusetts have all expressed concern and uncertainty in the days since Trump announced his ban.

MIT is urging its students to come back to campus immediately and offering them legal advice. In a statement, deans at MIT said they’re extremely concerned about the travel ban and they’re focusing on helping those who are directly affected.

Many institutions worry what might be next for the 15,000 students in the U.S. who come from the seven predominantly Muslim countries - Iraq, Syria, Iran, Yemen, Sudan, Libya and Somalia - named in Trump’s travel ban.

>> LISTEN: Bennington College President Speaks Out Against President Trump's Travel Ban

“This really is a balancing act,” said Terry Hartle, senior vice president with the American Council on Education, which represents hundreds of college presidents in Washington, D.C. “No college or university official is going to question the centrality of the federal government keeping the border secure.”

Hartle says Trump’s travel ban appears to have been put in place without input from the Department of Homeland Security and the Justice Department.

"The colleges and universities that I've spoken with are greatly confused about the meaning of the executive order, in part, because this order was rolled out quickly and apparently without careful assessment within the administration," Hartle said.

Despite widespread confusion and fear this weekend, Hartle points out that higher education has seen short periods of uncertainty for international students in the past.

After the September 11 attacks, there were calls to completely shut off international student visas to the United States. That never happened, but in 2002 the Bush administration did require residents of 25 Muslim-majority countries to report to the Department of Homeland Security and re-register for their visas.

Edward Alden, a senior fellow with the Council on Foreign Relations and author of “Failure to Adjust: How Americans Got Left Behind in the Global Economy,” says it's a shame that higher education is getting caught up in presidential politics.

Alden says Trump's isolationist, "America First" rhetoric is an awful message to send to the best and brightest around the world.

“There are a lot of people who are wary about immigration, worried about terrorism and quite justly aggrieved, I think, with some of the negative consequences of international trade,” Alden said in a phone interview Sunday. “But I would suspect that very few people understand the impacts that these sorts of measures are going to have.”

For now, Harvard Medical School student Samira Asgari is staying in Switzerland. She hopes her situation is resolved soon, but, if not, she might start looking for other opportunities in Canada, Germany or Australia.

“I’m a researcher,” Asgari said. “I really love my job, so if I cannot go to America I will pursue research elsewhere.”

While studying at Harvard Medical School was her dream, Asgari says she won’t give up on her career.